Millions of people in Japan have paid tribute to the thousands of victims of the earthquake and tsunami that devastated the country's north-east coast one year ago and sparked the world's worst nuclear crisis for 25 years.

At 2.46pm local time (5.46am GMT), a year on from the moment the magnitude-9.0 earthquake struck, people across Japan bowed their heads and observed a minute's silence, while sirens sounded in the dozens of coastal communities still in mourning for the 15,800 people confirmed dead and 3,300 others still missing.

In Tokyo, some train services came to a standstill, and the emperor, empress, prime minister, foreign dignitaries and hundreds of survivors attended a ceremony at the capital's national theatre.

In Ishinomaki, where the tsunami left more than 5,700 people dead or missing, hundreds attended a service at Minato primary school, where some had taken refuge after the disaster.

Many remained silent after the official silence, hands clasped in prayer as Buddhist monks chanted sutras before an altar laden with white chrysanthemums. As darkness fell, children lit paper lanterns bearing simple messages that resonate across the region: togetherness, hope and strength.

The people of the city, almost half of which was submerged beneath waves of up to 10 metres in height, are torn between two overwhelming emotions: deep sadness at the loss of life, and a determination to look forward.

Masaru Sasaki, a 71-year-old taxi driver, came to remember his wife, daughter and grandson, all swept away by the waves. "In some ways, the last 12 months have passed quickly," he said. "But when I think of my family, it seems like a lifetime.

"I am lucky enough to be able to work, and I gain strength each day from my passengers. If I didn't have that, I don't think I could go on living."

The prime minister, Yoshihiko Noda, vowed that Japan would be "reborn as en even better place".

"Our predecessors who brought prosperity to have repeatedly risen up from crises, every time becoming stronger," he said. "We will stand by the people from the disaster-hit areas and join hands to achieve the historic task of rebuilding."

It is impossible to overstate the size of that task. Exactly a year after they were sent fleeing by waves of up to 20 metres in height, more than 320,000 displaced people are still living in temporary housing along the north-east coast. An estimated 23m tonnes of rubble has been removed and placed in piles, but only a fraction has been buried or incinerated.

The cost of rebuilding dozens of cities, towns and villages on higher ground is expected to cost Japanese taxpayers $230bn (£145bn) over the next 10 years. Some of that will come from an expected doubling of the sales tax; rather less palatable, for many, are the tens of billions the government will spend to prop up the company at the centre of the nuclear crisis, Tokyo Electric Power (Tepco).

The sense of loss was tinged with bitterness at the slow pace of reconstruction and the government's handling of the crisis at the Fukushima Daiichi nuclear power plant.

On Friday, newly released government documents revealed that Japan's cabinet was aware of the imminent risk of a meltdown, but elected to suppress the information for weeks unless it sparked panic among the public. Tepco did not publicly acknowledge a partial meltdown in three reactors until May.

"I no longer trust the government," Ayumi Sato said as she left a memorial service in Ishinomaki cradling her baby daughter. "This disaster has made me realise that the only people capable of looking after our daughter's future are me and my husband."

Amid the solemnity came protest. In Fukushima prefecture and Tokyo, thousands turned out to demand the permanent closure of all of Japan's nuclear reactors. An estimated 12,000 protesters in the capital formed a human chain around the parliament building.

All but two of the country's 54 reactors are currently closed for maintenance checks, and will not be permitted to restart unless they pass tests of their ability to withstand catastrophic events and win approval from host communities spooked by the Fukushima accident.

The triple meltdown at Fukushima forced the immediate evacuation of 80,000 people living within 20km; a similar number have left other towns and villages outside the evacuation zone where high levels of radiation have been found.

The operation to decontaminate the area is expected to last years, and neighbourhoods closest to the plant could remain uninhabitable for decades.

In Tokyo, Emperor Akihito acknowledged the difficulties facing Fukushima's displaced residents. "In order to make the area inhabitable again, we face the difficult problem of removing radiation," the 78-year-old, who has recently undergone heart surgery, said in a brief address.

"We shall not let our memory of the disasters fade, pay attention to disaster prevention and continue our effort to make this land an even safer place to live."

After workers at Fukushima Daiichi observed a minute's silence, Tepco's president, Toshio Nishizawa, expressed his "heartfelt sympathy" to the victims of the disaster and apologised to residents living near the stricken plant.

"While always keeping in mind the tremendous responsibility we have to maintain stable conditions at the Fukushima Daiichi nuclear plant, we will continue to safely work toward the mid- to long-term decommissioning of the reactors.

"The day of 11 March is forever etched on the hearts and minds of every Tepco employee."

Many survivors chose to mark the day in private. Yuko Sugimoto, who became a symbol of the tsunami when she was photographed, draped in a blanket amid the wreckage, searching for her son, Raito, whose nursery was partly submerged.

Sugimoto and Raito, who had been rescued by the military from the nursery roof, were reunited two days later. A year on, life was beginning to return to normal, she said, but for her son, the mental scars had yet to heal.

"He won't let me leave him, even for a minute," she said at her new home outside Ishinomaki. "When we had tsunami warnings after 11 March he was physically sick. He's doing his best to appear normal, but I know that on the inside he is still in a great deal of pain."